The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing

BMC Genomics

Methodology Article

Walter Pirovano¹  Menno Schilthuizen²  Dick SJ Groenenberg³  Edmund Gittenberger⁴ 

[1] BaseClear B.V., P.O. Box 1336, 2302, Leiden, BH, The Netherlands;Institute of Biology, Leiden University, Sylvius Lab., P.O. Box 9505, NL 2300, Leiden, RA, The Netherlands;Netherlands Centre for Biodiversity Naturalis, P.O. Box 9517, 2300, Leiden, RA, The Netherlands;Netherlands Centre for Biodiversity Naturalis, P.O. Box 9517, 2300, Leiden, RA, The Netherlands;Institute of Biology, Leiden University, Sylvius Lab., P.O. Box 9505, NL 2300, Leiden, RA, The Netherlands;

关键词: Mitochondrial Fraction;    Museum Specimen;    CytB Sequence;    Terrestrial Snail;    Illumina GAIIx;   

DOI  :  10.1186/1471-2164-13-114

 received in 2011-10-07, accepted in 2012-03-26,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThis study describes how the complete mitogenome of a terrestrial snail, Cylindrus obtusus (Draparnaud, 1805) was sequenced without PCRs from a collection specimen that had been in 70% ethanol for 8 years. The mitogenome was obtained with Illumina GAIIx shot gun sequencing. Although the used specimen was collected relatively recently and kept in a DNA-friendly preservative (not formalin as frequently used with old museum specimens), we believe that the exclusion of PCRs as facilitated by NGS (Next Generation Sequencing) removes a great obstacle in DNA sequencing of collection specimens. A brief comparison is made between our Illumina GAIIx approach and a similar study that made use of the Roche 454-FLX platform.ResultsThe mtDNA sequence of C. obtusus is 14,610 bases in length (about 0.5 kb larger than other stylommatophoran mitogenomes reported hitherto) and contains the 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs) typical for metazoans. Except for a swap between the position of tRNA-Pro and tRNA-Ala, the gene arrangement of C. obtusus is identical to that reported for Cepaea nemoralis. The 'aberrant' rearrangement of tRNA-Thr and COIII compared to that of other Sigmurethra (and the majority of gastropods), is not unique for C. nemoralis (subfamily Helicinae), but is also shown to occur in C. obtusus (subfamily Ariantinae) and might be a synapomorphy for the family Helicidae.ConclusionsNatural history collections potentially harbor a wealth of information for the field of evolutionary genetics, but it can be difficult to amplify DNA from such specimens (due to DNA degradation for instance). Because NGS techniques do not rely on primer-directed amplification (PCR) and allow DNA to be fragmented (DNA gets sheared during library preparation), NGS could be a valuable tool for retrieving DNA sequence data from such specimens. A comparison between Illumina GAIIx and the Roche 454 platform suggests that the former might be more suited for de novo sequencing of mitogenomes.

【 授权许可】

CC BY   
© Groenenberg et al; licensee BioMed Central Ltd. 2012